On Tue, Mar 19, 2013, Marta Perez wrote:
> My question is: Why amber developers chose to put in the template this ONE
> conformation (and not other conformation from many possible conformations)?
> (Is it the most populated conformation based on all the PDB structures
> available? or ....?)
Sorry if I wasn't clear in my previous reply: Amber developers did not
"choose" anything. The templates were created thirty years ago, before there
was any notion of rotameric preferences in the PDB, for example. I'm
guessing (you can check) that most of the conformations are extended ones. You
should not rely on LEaP to add missing atoms, unless its choices are very
simple ones, or unless you don't care about the sorts of questions you are
asking.
...dac
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Received on Tue Mar 19 2013 - 08:00:04 PDT
